ENST00000586321.1:n.60+10685C>T

Variant names:

• chr17-78326473-C-T
• rs11651398
• ENST00000586321.1:n.60+10685C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586321.1(ENSG00000267737):​n.60+10685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,200 control chromosomes in the GnomAD database, including 477 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.070 (477 hom., cov: 31)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 4 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.098 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.73+10685C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.60+10685C>T		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.38+10685C>T		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.71+8485C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10672 AN: 152082 Hom.: 476 Cov.: 31

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0701

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0701 AC: 10671 AN: 152200 Hom.: 477 Cov.: 31 AF XY: 0.0683 AC XY: 5084 AN XY: 74418

African (AFR) AF: 0.0335 AC: 1393 AN: 41558

American (AMR) AF: 0.0517 AC: 790 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4822

European-Finnish (FIN) AF: 0.0741 AC: 785 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6797 AN: 67986

Other (OTH) AF: 0.0693 AC: 146 AN: 2106

Alfa AF: 0.0856 Hom.: 562

Bravo AF: 0.0652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.85
PhyloP100		0.96
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11651398; hg19: chr17-76322554;